In zhezhangsh/rchive:

knitr::opts_chunk$set(dpi=300, fig.pos="H", fig.width=8, fig.height=6, echo=FALSE, warning=FALSE, message=FALSE);

source_url<-"sftp-cancer.sanger.ac.uk/cosmic/grch38/cosmic/v75";
file_home<-paste(Sys.getenv('RCHIVE_HOME'), 'data/variant/public/cosmic/src', sep='/');
file_out<-paste(Sys.getenv('RCHIVE_HOME'), 'data/variant/public/cosmic/r', sep='/');

Source

• All source files were downloaded from: r source_url
• Downloaded files were unziped and saved to: r file_home for further processing
• Processed files were archived to: r file_out

##############################################################################################################
tm<-strsplit(as.character(Sys.time()), ' ')[[1]][1];
fn0<-paste(Sys.getenv("RCHIVE_HOME"), '/source/script/update/variant/ProcessCosmic.Rmd', sep='');
fn1<-paste(Sys.getenv("RCHIVE_HOME"), '/source/script/update/variant/log/', tm, '_ProcessCosmic.Rmd' , sep='');
file.copy(fn0, fn1)

END OF DOCUMENT

zhezhangsh/rchive documentation built on June 17, 2020, 3:55 a.m.